UP Mathematicians Develop Algorithm to Simulate Monkeypox Spread and Raise Awareness

UP Mathematicians Develop Algorithm to Simulate Monkeypox Spread and Raise Awareness

Published: February 22, 2024

By: Maria Alexandra Marmol

In a major stride towards enhancing global epidemic preparedness, Drs. Victoria May Mendoza and Renier Mendoza of the UP Diliman College of Science Institute of Mathematics (UPD-CS IM) have provided key findings on the dynamics of monkeypox spread. In collaboration with South Korean researchers, the team developed an innovative algorithm to investigate the pivotal role of self-reporting and contact tracing in the early stages of monkeypox transmission via simulations.

The stochastic simulation process illustrating the possible mitigation or spread of infection depending on whether the primary case self-reports or not. (Photo credit: Ko et. al., 2023)

Their findings, published in the Journal of Medical Virology, showcased that the most crucial element affecting the size of an outbreak and its potential duration is the behavior of the primary case—that is, the infected person carrying disease into a community, and whether or not they report their status for medical attention. 

 

The study followed as a result of a sudden monkeypox outbreak in non-endemic countries in May of 2022. Although the majority of the infected had had no history of travelling to the endemic areas of central and western Africa, the disease continued to spread, and more and more cases were still being reported worldwide.

 

In South Korea, however, the first case of an individual diagnosed with monkeypox had immediately self-reported in June 2022. After travelling to Europe and returning in the same month, the primary case informed the Korea Disease Control and Prevention Agency (KDCA) of his symptoms and contact history. Subsequently, there were no other recorded secondary infections of monkeypox within the country.

 

To study this scenario and the other factors affecting the potential outbreak of monkeypox in a non-endemic country, the team used a mathematical model based on Gillespie’s stochastic chemical kinetics. 

 

Stochastic models are quantitative techniques that take into account random variables when predicting possible outcomes. While these have commonly been used to analyze the effects of other infectious diseases, this marked the first time that a stochastic model was used to simulate the spread of monkeypox in a non-endemic country.

 

In this manner, their algorithm considered random fluctuations in human behavior and subsequent delayed contact tracing. They then set up eight scenarios for their study, running 100,000 simulations in each to better understand the significance and impact of the primary case’s self-reporting or lack thereof.

 

Through these simulated outbreaks, they projected the average numbers of infected individuals depending on whether the primary case self-reported or not. In the scenario wherein the primary case self-reported, the number of infected individuals only increased by 11%.

 

But in the scenario wherein the primary case did not self-report, thereby further delaying contact tracing, the number of infected individuals increased by up to 40%.

 

The large difference in results served as both clear evidence and cautionary tales of the dangers of unreported cases. By understanding the impact of the primary case’s and infectees’ behavior, the study provides a more intuitive analysis that healthcare authorities may use as guiding information in the management and detection of possible monkeypox outbreaks in the future.

 

However, the researchers believed that one of the many factors dissuading people from seeking medical help—therefore greatly affecting attempts to mitigate disease—was stigma.

“The social media coverage about monkeypox spread directly or indirectly generates racist and homophobic stereotypes that worsen stigma,” they explained in their paper. They emphasized that approaches to encouraging self-reporting should be based on rights and evidence to avoid situations of hidden infected cases.

 

“(…) healthcare authorities must ensure confidentiality of confirmed cases and individuals under investigation, and access to health services. Moreover, prompt case finding and information campaigns must be conducted,” they urged.

 

​​The World Health Organization (WHO) now intends to replace the term “monkeypox” with “mpox” due to the racist and stigmatizing language surrounding the disease online following the 2022 outbreak. The virus itself is transmittable either through animal-to-human or human-to-human contact with bodily fluids or any contaminated material. For the 2022 outbreak, the symptoms were largely flu-like, with rashes that started around the genital area—but unlike the rashes typical to monkeypox, they appeared more similar to measles or other noninfectious conditions.



For interview requests and other concerns, please contact media@science.upd.edu.ph. 



References:

Jang, Y. W., Lee, M., Shin, H., Kim, J., Choi, M., Kim, Y. M., Lee, M. J., Kim, J., & Na, H. K. (2022). The first case of monkeypox in the Republic of Korea. Journal of Korean Medical Science, 37(27). https://doi.org/10.3346/jkms.2022.37.e224

 

Ko, Y., Mendoza, V. M., Mendoza, R., Seo, Y., Lee, J., & Jung, E. (2023). Estimation of monkeypox spread in a nonendemic country considering contact tracing and self-reporting: A stochastic modeling study. Journal of medical virology, 95(1), e28232. https://doi.org/10.1002/jmv.28232


Mpox (monkeypox). (n.d.). https://www.who.int/news-room/questions-and-answers/item/monkeypox

Accelerating S&T in PH through Research: High-Impact Studies Led by UP Scientists in 2023

Accelerating S&T in PH through Research: High-Impact Studies Led by UP Scientists in 2023

Published: February 21, 2024

By: Eunice Jean Patron

Science and technology (S&T) play a vital role in Philippine development, providing innovative solutions to societal challenges faced by Filipinos. In that regard, the University of the Philippines – Diliman College of Science (UPD-CS) has been at the forefront of advancing S&T in the Philippines for decades, producing basic and applied scientific research of high standards and national relevance. Year after year, research spearheaded by UPD-CS scientists is published in various journals with high impact factors. The impact factor is a variable measuring a journal’s importance based on the average number of citations of its articles.


UPD-CS scientists continued the College’s long streak of quality research in 2023, with several studies they led becoming internationally recognized and included in some of the world’s most notable, high-impact journals. From examining Philippine tropical cyclones to the risk factors of breast cancer, here are some of UPD-CS’ recent scientific breakthroughs contributing to the country’s socio-economic development.

1. Analyzing the effects of pioneer colonizing bacteria on plastic breakdown in oceans

Once released into the environment, plastics become places where bacteria can attach and grow. The bacteria on plastic interact with each other and work differently than those in the surrounding environment, which can affect how plastics break down. However, little is known about specific types of bacteria that are the first to attach and interact with plastics.

 

Justine Marey Bitalac, Norchel Corcia Gomez, and Dr. Deo Florence Onda of the Marine Science Institute (MSI) studied bacteria from Manila Bay that attach to plastics. Their group identified ten types of bacteria, and the scientists tested their ability to grow on plastic over 60 days. The plastic showed signs of physical deterioration, and chemical analysis revealed that different species of bacteria potentially create varying changes in the plastic’s structure.


Bitalac and Dr. Onda’s research was published in the Journal of Hazardous Materials, a publication featuring articles in the areas of Environmental Science and Engineering. The Journal of Hazardous Materials has an impact factor of 13.6.

2. Detecting harmful dye pollutants using gold nanomaterials

Because of the abundant hot spots in their structure, branch-shaped gold nanomaterials are getting recognized as suitable enhancers for surface-enhanced Raman scattering (SERS), a technique typically used to detect toxic dye pollutants. However, making these nanomaterials usually involves time-consuming experiments that use hazardous and expensive chemicals.

 

Rufus Mart Ceasar Ramos of the Natural Sciences Research Institute (NSRI) and Dr. Michelle Regulacio of the Institute of Chemistry (IC) created gold nanomaterials using eco-friendly and low-cost organic acids in plants, such as ascorbic acid, oxalic acid, and tartaric acid. Their approach is also convenient, direct, inexpensive, and rapid, taking less than an hour to complete. The resulting branched gold nanomaterials, called nanocorals, also have numerous hot spots similar to the gold nanomaterials.


Ramos and Dr. Regulacio’s research was published in ACS Applied Nano Materials, a publication featuring research covering all aspects of engineering, chemistry, physics, and biology relevant to applications of nanomaterials. ACS Applied Nano Materials has an impact factor of 5.9.

3. Discovering the link between stress, altered light-dark cycles, and breast cancer

Disruption of the body’s 24-hour pattern of biological activity, known as the circadian cycle, is linked to an increased risk of breast cancer. Shift work and constant jet lag, in particular, have been associated with this risk.

 

In their study, Weand Ybañez and Dr. Pia Bagamasbad of the National Institute of Molecular Biology and Biotechnology (NIMBB) found out that a gene that suppresses tumor growth called the Krüppel-like factor 9 (KLF9) is downregulated in breast tumors compared to normal breast tissue. This gene’s activity is influenced by stress hormones and oscillates with the 12-hour light-dark cycle.  


Ybañez and Dr. Bagamasbad’s study was published in Cancer Cell International, a publication featuring studies on cancer cell biology originating from work using laboratory experiments. Cancer Cell International has an impact factor of 5.8.

4. Investigating quantum spin Hall and Rashba effects in flat ilmenite oxides

Inspired by the discovery of an excellent conductor of electricity called graphene, scientists became interested in other two-dimensional (2D) materials that can be used for technological applications. One of these 2D materials is ilmenite oxides.

 

A group of physicists, including Dr. Genevieve Macam of the National Institute of Physics (NIP), studied the properties of 2D ilmenite oxides with different metal combinations in their original and Janus forms, which are nanoparticles with two distinct surfaces. Their research showed that the different combinations with 2D ilmenite oxides could have applications in spin transport electronics, a branch of electronics that relies on the intrinsic spin of electrons for information storage and processing.


Dr. Macam’s research was published in the Chinese Journal of Physics, a publication featuring research in various branches of physics. The Chinese Journal of Physics has an impact factor of 5.

5. Exploring the potential of Cu2O semiconductors paired with plasmonic metals

Metal–semiconductor nanocomposites, especially semiconductors combined with plasmonic metals like gold (Au) and silver (Ag), can be used for various applications across different fields. These combinations have unique optical properties that arise from their interactions with light and the movement of charge carriers within their structure.

 

Enrico Daniel Legaspi from the Materials Science and Engineering Program (MSEP) and Dr. Michelle Regulacio of the Institute of Chemistry (IC) examined the pairing of the copper(I) oxide (Cu2O) with Au and Ag. In the review, the scientists detailed the methods and adjustments used to pair the components. The review also explored how these combinations affect the optical and electronic properties of the nanocomposites in the context of photocatalysis, a process where light energy is used to drive a chemical reaction.


Legaspi and Dr. Regulacio’s review was published in Nanoscale Advances, a publication featuring research on nanoscience and nanotechnology. Nanoscale Advances has an impact factor of 4.7.

6. Assessing the response of severe Philippine tropical cyclones to a warmer climate

The Philippines frequently experiences tropical cyclones (TCs), often leading to casualties and significant damage to property due to strong winds, flooding, and rainfall. Understanding how climate change impacts TCs is important, given their socioeconomic consequences.

 

A group of meteorologists, led by Dr. Rafaela Jane Delfino and Dr. Gerry Bagtasa of the Institute of Environmental Science and Meteorology (IESM), observed how three severe TCs (Haiyan from 2013, Bopha from 2012, and Mangkhut from 2018) might change under future warmer climate conditions through the pseudo global warming (PGW) technique. The simulations show that the three TCs could become more intense with increases in maximum wind speeds. The potential impact of the TCs is also expected to be higher in the future.

 

Dr. Delfino and Dr. Bagtasa’s research was published in Climate Dynamics, a publication featuring high-quality research on all aspects of the dynamics of the global climate system. Climate Dynamics has an impact factor of 4.6.


Press release: https://science.upd.edu.ph/more-intense-typhoons-to-come-this-century-up-study-warns/

7. Developing a framework for deriving analytic steady states of biochemical reaction networks

Understanding the long-term behaviors of biochemical systems involves looking at their stable states, but deriving these states directly for complex networks can often be challenging. Recent research focuses on network-based approaches, particularly transforming intricate networks of chemical reactions within biological systems into another weaker form. This method, however, can be challenging for larger and more complex networks.

 

A group of scientists, led by Dr. Bryan Hernandez of the Institute of Mathematics (IM), addressed this difficulty by breaking down complex networks into smaller, independent subnetworks before transforming them. This method provided an effective approach to analyzing and comprehending complex biochemical systems.


Dr. Hernandez’ study was published in PLOS Computational Biology, a publication featuring research focused on understanding living systems at all scales through the application of computational methods. PLOS Computational Biology has an impact factor of 4.3.

8. Examining bottom simulating reflectors in the Manila Trench forearc and its implications on the presence of gas hydrates in the region

Occurrences of gas hydrates in active plate margins have been reported in various locations and have been studied as both a potential alternative energy resource and a threat to methane release. The Manila Trench forearc, close to active margins with likely methane-rich sediments, can be a model to understand gas hydrate formation and the geological preconditions influenced by tectonics and sedimentation processes.

 

A team of scientists, including Elisha Jane Maglalang, Dr. Leo Armada, Madeline Santos, Karla May Sayen, and Dr. Carla Dimalanta of the National Institute of Geological Sciences (NIGS), conducted the first study that investigates the Manila Trench region for indicators of gas hydrates, laying the foundation for future gas hydrate research in the area and exploring its potential as an energy resource and the geological hazards linked to gas hydrate dissociation in an active margin setting, such as submarine slope failures and methane release to the atmosphere. The scientists also reinterpreted existing seismic data from the Manila Trench to describe bottom simulating reflectors (BSRs), which are considered important seismic markers of the probable presence of gas hydrates.


Their study was published in Marine and Petroleum Geology, a publication featuring research covering marine and petroleum geology. Marine and Petroleum Geology has an impact factor of 4.2.

9. Looking into the hidden diversity and genetic variations in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef

Genetic research is revealing extensive hidden diversity in reef-building corals, suggesting that the diversity in these key reef organisms is much greater than previously thought. Endosymbiotic algae living inside coral hosts may also help corals adapt to environmental stress, adding another layer of genetic variation that isn’t limited by differences between coral species.

 

A team of biologists, led by Dr. Ambrocio Melvin Matias of the Institute of Biology (IB), examined the genetic variations in a common reef-building coral, Acropora tenuis, and its associated endosymbiotic algae across the entire Great Barrier Reef (GBR). Their research suggests that the environment plays a vital role in shaping the algae communities living with the corals, which could help them adapt to changes in their environment.


Dr. Matias’ study was published in Evolutionary Applications, a publication featuring research on taxonomic groups – from microbes to plants and animals. Evolutionary Applications has an impact factor of 4.1.

10. Delving into the possible leafy vegetables' distinctive biomolecular properties included in prehistoric southern Vietnamese cuisine

Vietnamese cuisine is considered one of the healthiest in the world, with the inclusion of leafy green vegetables as one of the factors. The vegetables grow in both terrestrial and aquatic habitats, and they can be further chemically distinguished based on the lengths of their waxy organic compounds. Finding these compounds in pottery vessels as organic residues suggests that ancient people used pottery to prepare these food sources.

 

A group of scientists, led by Dr. Michelle Eusebio of the Science and Society Program (SSP), conducted an organic residue analysis on sampled pottery vessels from three archaeological sites in Southern Vietnam. Their analysis revealed that Vietnamese people used a specific combination of terrestrial and aquatic leafy vegetables in their cooking. They found a series of mid-to-long-chain fatty acids, alkanes, alcohols, and a wax ester (tetracosanyl palmitate, C40) in the pottery, which hasn’t yet been reported in archaeological pottery samples. This discovery provides new evidence on how ancient Vietnamese people used pottery to prepare and serve plant-based foods.


Dr. Eusebio’s research was published in the Journal of Archaeological Science: Reports, a publication featuring research applying scientific methods to archaeological problems. The Journal of Archaeological Science: Reports has an impact factor of 1.6.

College of Science Students Voice Out Concerns at the CS-Wide Student Consultation

College of Science Students Voice Out Concerns at the CS-Wide Student Consultation

Published: February 20, 2024

By: Harvey L. Sapigao

CS students at the CS-Wide Student Consultation. (Photo credit: Leandro Sampang)

Tight academic calendar schedules, ineffective reading breaks, and slow responses to mental health needs are among the pleas of CS students in the student-led CS-wide consultation held at the National Institute of Physics Auditorium on February 12, 2024.

 

The student-led event, organized by the CS Student Council (CSSC), was an avenue for CS students to raise issues on the academic calendar, reading breaks, learning modes, and student welfare. “It’s important to gather these sentiments as we gear forward to a much better system and policies in the future,” CSSC Chairperson Zedwin Sta. Monica said.

 

One of the most common sentiments of students was the tight academic calendar schedules. The first-semester schedule, from September to January, only included a few days of holiday break. Some expressed concern that it had been too short to justify spending expensive travel fees to return home to their provinces. A few chose not to make the trip at all and used the break to catch up on requirements instead.

 

A few students suggested that a first-semester schedule of August to December, and a second-semester schedule of January to May, would provide for a better academic year where students can enjoy the holiday break without needing to worry about their academics.

 

Another sentiment of students is the ineffective reading break. “Parang reading nalang siya, wala nang break,” one student said, alluding to the deadlines and exams scheduled immediately after the reading break, which forced students to instead use the time to finish requirements and prepare for exams.

 

The one-week reading break, the students suggested, should be separate from the 16-week semester schedule to avoid compressing academic workloads and give students a genuine week to recharge.

 

Lastly, a few voiced out the need for a faster response on the psychological services of the University. One student recalled her experience of having to wait two months for a response from PsycServ, or UPD’s psychological services.

 

They suggested giving more funding to mental health services, that one guidance counselor should be available for each institute, and that the CS wellness center should be made active again.

 

A total of 55 undergraduate and graduate students from different institutes attended the CS-wide student consultation. “The discussion was successful because the participants are very insightful and participative in their focus group discussions,” Sta. Monica said.

 

The CS Administration will review the student’s concerns and present them at the next college assembly and university council meeting. “We also plan to aid the CS Admin, should they craft position papers, amendments to the policies, etc.” Sta. Monica added.

 

For interview requests and other concerns, please contact media@science.upd.edu.ph.

UP Atmospheric Physicist Takes to the Skies with NASA: Monitoring Air Quality on NASA817

UP Atmospheric Physicist Takes to the Skies with NASA: Monitoring Air Quality on NASA817

Published: February 15, 2024

By: Maria Alexandra Marmol

(Photo credit: Dr. Gerry Bagtasa, 2024)

Dr. Gerry Bagtasa of the UP Diliman College of Science – Institute of Environmental Science and Meteorology (UPD – CS IESM) took flight with NASA last Sunday, February 11, 2024, as part of an air pollution measurement campaign called ASIA-AQ (Airborne and Satellite Investigation of Asian Air Quality). 

 

NASA817—more specifically the NASA DC-8 plane—is an airborne science laboratory based in NASA’s Armstrong Flight Research Center in Palmdale, California. It is flown to other parts of the world to gather data to support the research and experiments undertaken by the global scientific community.

 

The objective of this particular series of flights with the Filipino team, consisting of DENR-EMB, the Manila Observatory, and Dr. Bagtasa, was to assess the air quality of multiple Asian cities by utilizing satellite remote sensors and air quality models. With the equipment of the modified Douglas DC-8 jetliner, they were able to observe the atmosphere and detect various pollutants such as particulate matter, ozone, carbon dioxide, and methane, which are not usually locally measured above the ground.

 

“The purpose is to improve our understanding of the dynamics of air pollution in the region,” Dr. Bagtasa said. 

 

With the Filipino team, they were able to help plan the flights by providing air quality and weather forecasts. They also provided insights into local weather patterns, drawing from Dr. Bagtasa and the Manila Observatory’s recent publications and expertise in contextualizing the data being collected.

Flight path of the 8-hour trip around Metro Manila and surrounding regions flying alternately between 1000 ft and 10,000 ft. (Photo credit: Dr. Gerry Bagtasa, 2024)

The Experience

 

NASA817 flew four times to the Philippines on February 6, 7, 11, and 13, and for each flight, there were a few available seats for observers. Dr. Bagtasa and scientists of the Manila Observatory and DENR joined different flights, and of the 8-hour experience, the plane would constantly change altitudes from 1000 ft to 10,000 ft, then back again, to gather more data at different levels of elevation throughout the region.

 

“In almost any airplane ride, we encounter some brief bumpy to very bumpy, turbulent moments, right? Imagine that happening for 8 hours—the flight was brutal. I guess mainly due to the low-altitude nature of the flight,” Dr. Bagtasa commented. “And to make it more exciting, I experienced the hardest of hard turns and rolls in an airplane during the flight.” 

 

With humor, he also went on to say, “Most of the researchers on the plane wear some transdermal patch behind the ear for motion sickness. I didn’t, and I was in the backmost seat. After around 5 – 6 hours into the flight, considering that I’ve been on probably >100 flights in my lifetime, it was my first time to throw up in a plane ride.”

(Photo credit: Dr. Gerry Bagtasa, 2024)

Despite the bumpy ride, the flights are crucial to the campaign, ASIA-AQ. NASA’s project presents an avenue for international cooperation, partnering with local scientists, researchers, and experts to implement a unified strategy across various Asian nations in addressing not only regional air quality concerns but also gaining a broader understanding of the interpretation of satellite data and air quality modeling. 

 

Dr. Bagtasa and the Manila Observatory partnered with the DENR to join the flights to provide their local knowledge on the air pollution of the country. While the data gathered on these trips are still being processed and have yet to be published, NASA817 will now move on to South Korea, taking measurements in Taiwan on the way. After Seoul, it will then fly to Malaysia and Thailand. After the ASIA-AQ campaign, the NASA DC8 will be retired.

 

For interview requests and other concerns, please contact media@science.upd.edu.ph. 


References:

ASIA-AQ. (n.d.). https://espo.nasa.gov/asia-aq

NASA. (2023, September 29). DC-8 Airborne Science Laboratory – NASA. NASA. https://www.nasa.gov/centers-and-facilities/armstrong/dc-8-aircraft/

UP Physicists Present Network Science Research at the House of Representatives

UP Physicists Present Network Science Research at the House of Representatives

Published: February 13, 2024

By: Harvey L. Sapigao

Dr. Reinabelle Reyes and Dr. May Lim at the House of Representatives. (Photo credit: House Committee on Visayas Development)

Dr. Reinabelle Reyes and Dr. May Lim of the UP Diliman National Institute of Physics (UPD-CS NIP) presented their research on transport network efficiency at the recent House Committee on Visayas Development meeting on February 6, 2024.

 

Together with independent researcher JC Albert Peralta, Dr. Reyes and Dr. Lim used a 300-year-old math discipline called network science to model transport network systems during relief operations. They applied their model to the Visayas transport network, where they discovered that Northern Samar is the most vulnerable to relief operation delays. 

 

Read more about their research in the press release here: https://science.upd.edu.ph/up-physicists-improve-phls-disaster-response-with-network-science/


Their research opens novel ways for improving relief operations and aids policymakers in decision-making and strategic planning. Attendees of the meeting at the House of Representatives included committee leaders and members of the Visayas Region, including Hon. Karen Lolita Javier, Committee Chair and 2nd District of Leyte Representative; Hon. Francisco “Kiko” Benitez, 3rd District of Negros Occidental Representative; Hon. Anna Victoria Veloso-Tuazon, 3rd District of Leyte Representative; Francisco “Sonny” Romuar III, Committee Secretary; and Atty. Cherry Pastor-Dalauiadao, Committee Staff.

Leaders of the Visayas Region, together with Dr. Reyes and Dr. Lim. (Photo credit: House Committee on Visayas Development)

At the meeting, they discussed the need to decentralize and distribute resources such as food and key equipment to all congressional districts to mitigate delays in relief operations. They also emphasized the necessity of building transportation infrastructure in areas with no existing road networks.

 

“It was our first time at the House of Representatives and, though it was a bit intimidating at first, I believe in the end, we made the most of the opportunity given to us to share our work and learn from the perspectives of the House committee members, who are representatives and influential leaders for Visayas,” Dr. Reyes said on their experience.

 

“Doing scientific research is a very focused activity and involves discussion mostly among our small group of collaborators (and peer reviewers),” Dr. Reyes continued. “So having this opportunity to take the fruits of this work to the highest levels of leadership in the country is quite fulfilling at a different level.”

 

The research team aims to continue working on their research, developing an open-source, user-friendly web app that lets the public simulate different relief distribution scenarios. Dr. Reyes and Mr. Peralta will present their work at the upcoming PyCon PH 2024 conference on February 25 and 26, 2024.


For interview requests and other concerns, please contact media@science.upd.edu.ph.

Hiring! Student Assistants

Hiring! two (2) Student Assistants

📣 More student assistants needed! 📣

 

The Office of Associate Dean for Student, Alumni and Public Affairs (OADSAPA) of the College of Science is looking for two (2) Student Assistants.

 

Qualifications include:

– Must be a bona fide student of the College of and enrolled in the 2nd semester of A.Y. 2023-2024

– Must not be enrolled in more than 18 units during the semester of appointment

– Must not have any pending disciplinary cases in the University

– Responsible and must be aware of time management

 

Requirements for Application:

1. Curriculum Vitae (CV)

2. Copy of latest validated Form 5 (2nd Sem A.Y. 2023-2024)

3. Copy of previous semester’s grades (freshment exempted on this requirement)

4. Letter of Intent address to Dr. Giovanni A. Tapang

5. Sample works (writing, graphics)

6. Scanned copy of accomplished application form (

https://science.upd.edu.ph/wp-content/uploads/2023/09/Scholarship-Form.pdf )

 

Interested? Fill up the Google Form:

bit.ly/CSStudentAssistant2023
 
 

🙌 The deadline of application is February 05, 2024.

Paint by Numbers: UP Mathematician Formulates Rules in Modeling Crystal Structures

Paint by Numbers: UP Mathematician Formulates Rules in Modeling Crystal Structures

Published: January 29, 2024

By: Harvey L. Sapigao

Different ways of coloring a pattern. (Photo credit: Junio, A. O. Colorings of patterns fixed by an arbitrary finite-index subgroup of the Symmetry Group. Acta Crystallographica Section A Foundations and Advances, 79(6): p.558.)

Imagine yourself standing on a concrete floor. Your goal is to completely cover the floor with red and blue square tiles, but in a way that follows three rules: 

 

1) Every time you step on a tileless area, you must lay a tile. You can place either a red or blue tile on your starting position.

2) When you move one step horizontally or vertically, you must place a tile that is not the same color as the one you left. For example, if you started on a red tile and moved right, left, up, or down, lay a blue tile on your new location.

3) When you move one step diagonally, you must place a tile with a similar color to the tile you left. If you were standing on a red tile and moved diagonally, lay a red tile.

 

Once you have covered the floor with tiles, you will have created a colored checkerboard pattern. More interestingly, you will have also created a 2D model for the structure of salt crystals, which consists of alternating sodium and chlorine atoms: Red tiles can represent sodium atoms, while blue tiles can represent chlorine atoms.

 

Coloring a pattern such as the checkerboard is simple, but it becomes more complicated as patterns become more intricate. Dr. Allan Junio of the UP Diliman College of Science Institute of Mathematics (UPD-CS IM) created a technique that systematically colors patterns, helping model the structures of crystals.

 

Much like the three-step process in tiling the floor, Dr. Junio’s technique involves a set of general mathematical rules, called theorems and lemmas, in coloring different patterns. Moreover, his method enumerates all possible ways a pattern can be colored while limiting the number of colors used.

 

“The reason for this restriction is that we will be applying the coloring framework on the atoms of crystal structures, where the colors correspond to exactly one kind of atom, and we will be dealing with crystal structures with only finitely many kinds of atoms,” Dr. Junio explained in his paper.

 

The technique can help model a process called ordered substitution, where a group of atoms are replaced with a different element, thereby deriving a new material.

 

To demonstrate, he applied his technique to sphalerite crystal – a mineral that is difficult to identify due to its similarity with other crystals, hence its name coming from the Greek word sphaleros, meaning “treacherous.” Sphalerite is commonly made up of zinc and sulfur atoms linked together in a pattern.

Paint-by-Numbers-image1
Model for the structure of sphalerite. Zinc atoms are colored green, red, and blue, while sulfur atoms are colored black. (Photo credit: Junio, A. O. Colorings of patterns fixed by an arbitrary finite-index subgroup of the Symmetry Group. Acta Crystallographica Section A Foundations and Advances, 79(6): p.555.)

Instead of representing all zinc atoms with only one color, he colored different groups with green, red, and blue. In doing so, ordered substitution becomes simpler: by replacing the blue zinc atoms with copper atoms, the green zinc atoms with iron atoms, and the red zinc atoms with tin atoms, a new material called stannite is produced. Other crystals such as kuramite and chalcopyrite can also be produced using a similar process.

 

Although only sphalerite and its derivatives are modeled in the paper, the technique can be applied to other crystals as well.

 

“It may be a good idea to determine whether the resulting colorings correspond to known compounds, and if no such compounds exist, to establish whether the colorings may be realized as physical structures using chemical and molecular properties and restrictions,” Dr. Junio concluded in his paper, which is now published in Acta Crystallographica.

 

For interview requests and other concerns, please contact media@science.upd.edu.ph. 

Reference:

Junio, A. O. (2023). Colorings of patterns fixed by an arbitrary finite-index subgroup of the Symmetry Group. Acta Crystallographica Section A Foundations and Advances, 79(6), 550–559. https://doi.org/10.1107/s2053273323007878

Top 10 publications of UPD College of Science in 2023

Top 10 publications of UPD College of Science in 2023

Published: January 25, 2024

By: Harvey L. Sapigao

In 2023, about 1 in 20 studies produced by the Philippines came from the UP Diliman College of Science (UPD-CS). With a total of 368 studies across all scientific disciplines, UPD-CS studies accounted for more than half of the total publications produced by UP Diliman. This number comes as no surprise since the College is home to 211 Ph.D faculty members. But beyond the numbers, UPD-CS has published groundbreaking research in many prestigious research journals.

 

Here are the Top 10 studies published by UPD-CS scientists in journals with high Impact Factors (IF)*:

 

1. Shedding Light on Mysterious Superconductors (IF: 41.2)

 

Superconductors allow electricity to pass through with no resistance. Previously, it was believed that when excessive electrons are removed from a mysterious type of superconductor called  cuprate superconductor, known as “overdoping,” the material would behave in accordance with the Bardeen–Cooper–Schrieffer (BCS) theory. However, Dr. Miguel Sulangi of the National Institute of Physics and collaborators from the Netherlands, Japan, China, and the USA showed that this is not the case, challenging the long-held belief that BCS theory governs overdoped cuprate superconductors. Cuprate superconductors were discovered in 1986 but physicists have yet to uncover all its secrets.

 

Read the press release here: https://science.upd.edu.ph/upd-cs-nip-physicist-co-authors-groundbreaking-research-on-mysterious-superconductors/ 

 

Title: Puddle formation and persistent gaps across the non-mean-field breakdown of superconductivity in overdoped (Pb,Bi)2Sr2CuO6+δ

Journal: Nature Materials

DOI: https://doi.org/10.1038/s41563-023-01497-1

 

2. Applying Einstein’s Concepts of Relativity to Exotic Particles (IF: 16.6)

 

Einstein’s Theory of Relativity claims that two events can only influence one another if they are inside each other’s spacetime area called the light cone. Borrowing this concept, Dr. Gennevieve Macam of the National Institute of Physics worked with an international team of researchers to explain how two exotic particles called Weyl fermions interact. Their study is the first to describe Weyl fermions in terms of spacetime concepts, demonstrating how two physics disciplines – condensed matter physics and high-energy physics – are fundamentally connected.

 

Read the press release here: https://science.upd.edu.ph/beyond-einstein-pinay-physicist-investigates-exotic-subtonic-particles/ 

 

Title: Causal Structure Of Interacting Weyl Fermions In Condensed Matter Systems

Journal: Nature Communications

DOI: https://doi.org/10.1038/s41467-023-37931-w

 

3. History of Single-celled Predators (IF: 15.9)

 

Single-celled organisms, like the protists Acanthamoeba and Dictyostelium, use metals to kill bacterial prey. Exactly how these organisms evolved is the focus of the study by Dr. Windell Rivera and collaborators from China. They provided a timeline for the evolution of metal-poisoning protists, from the moment protists were created to the time they adapted to the environment and acquired the ability to use metals in killing their prey.

 

Title: A Brief History Of Metal Recruitment In Protozoan Predation

Journal: Trends in Microbiology

DOI: https://doi.org/10.1016/j.tim.2023.11.008 

 

4. Identifying First Bacteria Colonizers on Plastics (IF: 13.6)

 

Many types of bacteria live on plastics left in the environment. But for diverse colonies to thrive, a group of bacteria, called primo-colonizers, must first prime the plastics to make them habitable for other types of bacteria. Justine Marey Bitalac, Norchel Corcia Gomez, and Dr. Deo Florence Onda of the Marine Science Institute, together with Dr. Nacita Lantican of UP Los Baños, identified these primo-colonizers and described how they change the structure of plastics. Their study helps elucidate how plastics degrade in the environment and opens possibilities on how to solve the growing plastic pollution problem.

 

Title: Attachment Of Potential Cultivable Primo-Colonizing Bacteria And Its Implications On The Fate Of Low-Density Polyethylene (LDPE) Plastics In The Marine Environment

Journal: Journal of Hazardous Materials

DOI: https://doi.org/10.1016/j.jhazmat.2023.131124

 

5. Simulating the Spread of Monkeypox (IF: 12.7)

 

Together with South Korean scientists, Drs. Victoria May Mendoza and Renier Mendoza of the Institute of Mathematics investigated the importance of self-reporting and contact tracing in controlling epidemics. They simulated how self-reporting and contact tracing affect the spread of monkeypox in non-endemic regions. They found out that an unreported primary case with delayed contact tracing can potentially increase the average number of infections by up to 40% compared to when the primary case is known and contact tracing is immediate.

 

Title: Estimation Of Monkeypox Spread In A Non-Endemic Country Considering Contact Tracing And Self-Reporting: A Stochastic Modeling Study

Journal: Journal of Medical Virology

DOI: https://doi.org/10.1002/jmv.28232

 

6. Classifying Seaweeds in the Philippines (IF: 11.5)

 

Seaweeds such as the milyon-milyon, tambalang, and kab-kab are abundant in the Philippines, making the country one of the leading seaweed farming industries in the world. Despite this, Philippine seaweeds are undocumented. Bea Crisostomo, Zae-Zae Aguinaldo, Lourie Ann Hinaloc, and Dr. Michael Roleda of the Marine Science Institute established the taxonomy and distribution of different seaweeds in the Philippines using knowledge from local farmers. Their study provides a database of seaweeds that can be used for conservation efforts.

 

Title: The Diversity Of Eucheumatoid Seaweed Cultivars In The Philippines

Journal: Reviews in Fisheries Science & Aquaculture

DOI: https://doi.org/10.1080/23308249.2022.2060038

 

7. Tropical Cyclones and their Threat to Food Security, Health, and Biodiversity (IF: 11.1)

 

Damages brought by tropical cyclones produce a cascading effect on food security, health, and biodiversity. In a perspective paper by Dr. Rene Abesamis of the Marine Science Institute and collaborators from Chile, Japan, Switzerland, and Norway, they explained that tropical cyclones can damage roads, agricultural infrastructure, and grazing lands, which affects food production. The destruction of tropical ecosystems also affects food security, which in turn produces health problems such as micronutrient deficiency. The authors urge researchers to develop tools that can aid in policy-making and governments to coordinate closely in a collaborative effort to curb the effects of tropical cyclones.

 

Title: Impacts Of Tropical Cyclones On Food Security, Health And Biodiversity

Journal: Bulletin of the World Health Organization

DOI: http://dx.doi.org/10.2471/BLT.22.288838

 

8. Tracking Human Settlers in the Holocene Period Using Genetics (IF: 11.1)

 

By analyzing almost two decades’ worth of genomic data, Jae Joseph Russell Rodriguez of the Natural Sciences Research Institute and international researchers traced how humans migrated around the world and how they facilitated the spread of language and agriculture about ten thousand years ago. In Southeast Asia, their study suggests that human settlers in the region, referred to as Austronesians, first migrated from China to Taiwan, then moved southward to the Philippines, Indonesia, and Papua New Guinea. Using sophisticated boating technology, Austronesians were then able to reach islands as far as Madagascar and Hawaii.

 

Title: Genomic Perspectives On Human Dispersals During The Holocene

Journal: Proceedings of the National Academy of Sciences

DOI: https://doi.org/10.1073/pnas.2209475119

 

9. Water-purifying Nanoparticles (IF: 9.9)

 

As water pollution becomes an ever-more pressing issue, we are in dire need of technologies that can purify water. Dr. Michelle Regulacio of the Institute of Chemistry collaborated with scientists from China to create a nanocomposite that can get rid of water contaminants with the help of light. The nanocomposites, made up of zinc oxide and carbon, can easily cling to organic dyes and bacteria and, using energy from light, decompose or kill them. The nanocomposites are cheap and simple to manufacture, offering a cost-effective wastewater treatment system.

 

Title: Hydrophilic ZnO/C Nanocomposites With Superior Adsorption, Photocatalytic, And Photo-Enhanced Antibacterial Properties For Synergistic Water Purification

Journal: Journal of Colloid and Interface Science

DOI: https://doi.org/10.1016/j.jcis.2023.06.019

 

10. Marine Pollution and Its Effects on Southeast Asian Biodiversity (IF: 9.8)

 

Southeast Asia is one of the most biodiverse regions in the world while also contributing significantly to marine pollution. Yet the region is underrepresented in studies that focus on the effects of marine pollution on biodiversity. In their review paper, Dr. Lemnuel Aragones of the Institute of Environmental Science and Meteorology and partners in Southeast Asia investigated why this is the case. They found out that these sorts of studies are complicated by language barriers, sociocultural limitations, and difficulties in examining species.

 

Title: Interactions Between Marine Megafauna And Plastic Pollution In Southeast Asia

Journal: Science of The Total Environment

DOI: https://doi.org/10.1016/j.scitotenv.2023.162502

 

In addition, here are the top studies published by UPD-CS-affiliated authors in high IF journals:

 

Using Algorithms to Model Social Behaviors (IF: 11.25)

 

Algorithms such as machine learning (ML) are better at classifying social responses than conventional statistical tools. That’s what Dr. Armando Apan of the Institute of Environmental Science and Meteorology (IESM) and collaborators from Nepal concluded in their research that looked upon the perspective of Nepalese people on energy consumption. ML models of public perceptions can aid in policy-making, planning, and implementation.

 

Title: Application Of Machine Learning To Assess People’s Perception Of Household Energy In The Developing World: A Case Of Nepal

Journal: Energy and AI

DOI: https://doi.org/10.1016/j.egyai.2023.100303

 

Examining Ecosystem Services in the Himalayas (IF: 11.1)

 

Services from nature like water supply, crop production, and habitat quality are called ecosystem services. Ecosystem services have unique relationships with one another. For example, when farmers convert forests into farms to increase crop production, the habitat quality will decrease. These unique relationships are the research focus of Dr. Armando Apan of the IESM and his partners in Nepal. They looked into how each ecosystem service changes with respect to one another and examined how this affects the ways of living in the Himalayas.

 

Title: Understanding Production Possibility Frontiers And Utility Values Of Ecosystem Services In The Himalayas: An Analysis Of The Supply-Demand Divide

Journal: Journal of Cleaner Production

DOI: https://doi.org/10.1016/j.jclepro.2023.138725

 

Why Renewable Energy Sources are Failing in Nepal (IF: 9)

 

The threat of climate change urges countries to transition to renewable energy sources, but developing countries such as Nepal struggle to do so. Dr. Armando Apan of the IESM and collaborators from Nepal examined the reasons and learned that solar and wind technologies shut down because of poor planning and fund discontinuation. Dr. Apan and collaborators emphasized the need to tackle the issue using “bottom-up” approaches that consider local contexts rather than “top-down” approaches that only look at the issue as mere technological transfers.

 

Title: Rationalizing donations and subsidies: Energy ecosystem development for sustainable renewable energy transition in Nepal

Journal: Energy Policy

DOI: https://doi.org/10.1016/j.enpol.2023.113570

 

* The metric Impact Factor (IF) measures the average number of times research papers are cited. For example, a journal with an IF of 9 means that, on average, research papers published in that journal are cited 9 times.

UP Chemists Modify Anticancer Compound to Improve Safety and Efficacy

UP Chemists Modify Anticancer Compound to Improve Safety and Efficacy

Published: January 23, 2024

By: Harvey L. Sapigao

Chemical structure of deguelin. (Photo credit: Francisco, J. A., & Paderes, M. C. Inhibitory effects of B-, C-, and E-ring-truncated deguelin derivatives against A549, HCT116, and MCF-7 Cancer Cells. ACS Omega, 8(45): p. 43109–43117)

Scientists from the University of the Philippines – Diliman College of Science (UPD-CS) have transformed the anticancer compound deguelin into a novel class of compounds that show promise as safer and more effective treatments for colon, lung, and breast cancer.

 

Originally used as a pesticide and fish poison, concerns arose regarding the safety of administering deguelin to humans once it was identified as a cancer treatment. Science Research Specialist John Alfon Francisco and Dr. Monissa Paderes of the UPD-CS Institute of Chemistry (UPD-CS IC) addressed these concerns by altering the structure of deguelin.

 

Their altered versions exhibited better qualities than the original compound. Preliminary tests done on human cancer cell cultures revealed reduced adverse effects, prompting Dr. Paderes and collaborators to conduct further research into the safety of these compounds.

 

Some versions are also more effective against specific types of cancer. “We were amused to find that some compounds have improved anticancer properties than its parent compound, deguelin, with some even surpassing the effectiveness of the commercially available anticancer drug doxorubicin,” Francisco said. For instance, a version named 6a outperformed doxorubicin in treating colon cancer, while versions 3a and 8e excelled in treating lung and breast cancer, respectively.

 

Their modified versions offer a simpler and more cost-effective production than those developed in previous studies. “The simplicity of the structures, as well as the straightforward synthesis of these compounds, add to the novelty of this study,” Dr. Paderes emphasized.

 

The researchers created the altered versions by shortening a part of deguelin known as the BCE ring, making the new versions more akin to the deoxybenzoin compound, recognized for its antibacterial and antioxidant properties.

 

Despite its huge commercial potential, their research is still in its early stages. The next phase involves testing the modified anticancer compounds on animal models. If the compounds are proven effective on animals, it will move on to clinical trials, where it will be tested on humans with colon, lung, or breast cancer. If proven successful, the Food and Drug Administration (FDA) will review and approve the rollout of the compounds as cancer treatments.

 

“The goal would be to advance these compounds toward clinical trials and potential development as novel anticancer therapeutics,” Dr. Paderes concluded.

 

For interview requests and other concerns, please contact media@science.upd.edu.ph. 



References:

Francisco, J. A., & Paderes, M. C. (2023). Inhibitory effects of B-, C-, and E-ring-truncated deguelin derivatives against A549, HCT116, and MCF-7 Cancer Cells. ACS Omega, 8(45), 43109–43117. https://doi.org/10.1021/acsomega.3c06619

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